Another Evolution Fairy Tale? Canning and putting away Darwinism.

Recent conversations have revealed that the average Darwinist who comments on this blog is far more devout to Darwinism than they are to science. Darwinists have insisted that the Law of Biogenesis is not a law, even though it was declared a law in peer reviewed papers and official meetings and their publications after years of testing for, not just higher forms of life, but for the simplest of microbes. Louis Pasteur (known in part for Pasteurization) was one of the leading 19th Century scientists who established this law after rigorous testing that went on for decades by many scientists. No one ever found life coming from non-life. Take a look at the evidence for yourself...

This is why pasteurization/sterilization and vacuum-packing of foods for storage on shelves is possible. Since operational science has proven that life does not come from non-life, sterilizing and sealing off food from any source of contamination guarantees that no deadly bacteria will grow within the can of food unless the seal is broken. So any Darwinist who believes that canned food is safe is saying that he believes in abiogenesis but he is betting his health and perhaps his very life on the fact that abiogenesis will not happen! So my commenters are not practicing what they preach, so to speak.

To come up with life, you need an organism that has the "spark of life" and is capable of reproducing itself. If it is not self-replicating, it could not be a source of life. It also must be able to metabolize something and convert it to energy upon which it would live. Now, the simplest self-replicating organism I am aware of is a Mycoplasma genitalium, which is composed of 482 genes and 580,000 DNA letters or necleotides and it is a parasite that cannot survive alone. Nanoarchaeum equitans is credited with only 490,885 letters but it is not well studied and documented yet. Carsonella ruddiiis also a candidate for being a complete life form that, to my knowledge, has not been proven to survive on its own. How much more complex must life be to survive without being a parasite? I will include a Sarfati article concerning this farther down the line.

Whatever that simplest life form might be,it will be composed of many hundreds of thousands of components and many hundreds of thousands of DNA letters in its DNA strand and from what we know of DNA, we know that it does not simply get "read" like a book but it is expressed in multiple ways during the process of reproduction. So the simple cell is hardly simple at all.

Michael Denton, in his book "Evolution, a Theory in Crisis", said: "To grasp the reality of life as it has been revealed by molecular biology, we must magnify a cell a thousand million times until it is twenty kilometers in diameter and resembles a giant airship large enough to cover a great city like London or New York. What we would then see would be an object of unparalleled complexity and adaptive design. On the surface of the cell we would see millions of openings, like the port holes of a vast space ship, opening and closing to allow a continual stream of materials to flow in and out. If we were to enter one of these openings we would find ourselves in a world of supreme technology and bewildering complexity."

Denton wrote those words in 1986. Since then we have found that the cell is much more intricate that Denton knew even at that time, approximately a quarter of a century before today. But those seeking a way to find a naturalistic source for life have done no better than Miller and Urey did in 1953. All so-called "primordial soups" that might produce one small portion of a DNA or RNA strand is always destroyed by the nature of the soup itself or incapable of building forward into DNA or RNA for chirality reasons or because of the presence of oxygen and/or many other obstacles along the way. The raw building blocks of DNA do not live well "in the wild" at all.

In fact, in an RNA world you still have the problem of racemic sugars that would form naturally if they did at all but RNA requires homochirality as in right-handed. Also sugars need reactive formaldehyde to form in nature and formaldehyde reacts with almost anything so it is highly unstable and deadly to proteins. Sugars are, by the way, very unstable in high temperatures, which shoots the "life formed in deep sea vents" idea in the head. The fact is that these extremophiles have very efficient correction machinery to continually replace components broken down by the high heat of smoker vents. So the symbiotic ecosystems of smokers may look primitive but are in fact quite advanced when you get down to the micro and molecular level.

Some Darwinists claim that "natural selection" operated on random chemicals to help form the first cell, but natural selection is associated with part of the process of reproduction and is therefore limited to already living beings. There is no "natural selection" operating amongst chemicals.

Hubert Yockey, certainly no creationist, said this about abiogenesis or what is sometimes called chemical evolution in 1992: "Although at the beginning the paradigm was worth consideration, now the entire effort in the primeval soup paradigm is self-deception on the ideology of its champions. … The history of science shows that a paradigm, once it has achieved the status of acceptance (and is incorporated in textbooks) and regardless of its failures, is declared invalid only when a new paradigm is available to replace it. Nevertheless, in order to make progress in science, it is necessary to clear the decks, so to speak, of failed paradigms. This must be done even if this leaves the decks entirely clear and no paradigms survive. It is a characteristic of the true believer in religion, philosophy and ideology that he must have a set of beliefs, come what may (Hoffer, 1951). Belief in a primeval soup on the grounds that no other paradigm is available is an example of the logical fallacy of the false alternative. In science it is a virtue to acknowledge ignorance. This has been universally the case in the history of science as Kuhn (1970) has discussed in detail. There is no reason that this should be different in the research on the origin of life." (Yockey, H.P. Information Theory and Molecular Biology)

Yockey was, of course, saying there were no naturalist paradigms because he did not wish to consider that God created all things including life. It is a presupposition, a worldview choice rather than a scientific fact that causes Darwinists to avoid the obvious conclusions one draws from the evidence. In fact I will shotgun a few pieces of evidence that will make you shake your head in wonderment at Darwinists unless you are already a devout believer in Darwinism. Ordinary scientists would have long ago given up on chemical evolution as an impossibility if testing and trials were the forces fueling the search rather than religion.

Ribosomes are needed to decode DNA, but the instructions for making ribosomes are contained within the DNA Karl Popper said,"What makes the origin of life and of the genetic code is a disturbing riddle is this: the genetic code is without any biological function unless it is translated; that is, unless it leads to the synthesis of the proteins whose structure is laid down by the code. But...the machinery by which the cell...translates the code consists of at least fifty macromolecular components which are themselves coded into the DNA. Thus the code cannot be translated except by using certain products of its translation." (Studies in the Philosophy of Biology, U of California Press.)

DNA produces helical proteins and globular proteins and it is worth mentioning that proteins break down in water so even at this level of the process, before going into molecular chemistry, a DNA that develops in primordial soup is unlikely anyway. In fact oxygen breaks up amino acids and the Miller-Urey experiment that produced a few amino acids only worked with a special protected chamber to segregate them from the conditions that produced them because those same conditions would immediately destroy those selfsame acids.

Enzymes are also a factor in expressing DNA, speeding up reactions by many magnitudes. One reaction essential in making the building blocks of DNA and RNA would take 78 million years in water, but a vital enzyme speeds it up 10 to the 18 times. Phosphotase speeds up reactions vital for cell signalling by 10 to the 21st times. It must be there for reactions that take place in a hundredth of a second in real life, for in a world without it one such reaction would take a trillion years! Such facts caused Richard Wolfenen to be quoted as recorded in the National Academy of Science 100 (May 13, 2003): "Without catalysts, there would be no life at all, from microbes to humans. It makes you wonder how natural selection operated in such a way as to produce a protein that got off the ground as a primitive catalyst for such an extraordinary long reaction."

It makes me wonder how Richard Wolfenen can call himself a scientist at all. Again, natural selection only operates on life forms, not on inorganic substances or sugars or proteins. Why bring natural selection into the conversation of how life could form when it cannot operate without life? Amazing brain cramp there.

Time for a note about complexity versus order versus random occurrence. Random occurrences are supposed to be the engine driving mutations that supposedly cause macroevolution in organisms, even though now that we are mapping genomes we are discovering that devolution is the problem facing life. Copying errors and mistakes are beginning to erode the gene pool of man and animal alike. The Human Genome Project showed us that a red-haired freckled girl from Ireland who has to jump to reach five foot tall and a seven-foot black man from Uganda will only vary about one per cent in comparing their DNA, but we can also see that mutations are degrading the DNA string and over time extinction would be expected if man cannot learn to reverse the trend. Too bad so many of them are listening for aliens or trying to prove abiogenesis instead of doing something worthwhile...Anyway, natural processes can produce repetitive patterns that have an orderly appearance, like crystals or fractals, along the line of ABCABCABC. But information is complex and coded, such as is the DNA string. No natural sources can be found for such coding. Yet we see complexity in enzymes like Myoglobin or the famous double sieve enzymeisoleucyl-tRNA synthase:

All living organisms contain literally encyclopedic quantities of complex, specific information. To store this information, living things have by far the most compact information storage/retrieval system known: the nucleic acid/protein system. The master blueprint or recipe is coded on enormous molecules of DNA (deoxyribonucleic acid).1 A codon, or sequence of three of the four types of DNA ‘letters’ (nucleotides), codes for one of the 20 types of protein ‘letters’ (amino acids). A gene is defined as a sequence of nucleotides coding for a single protein, or a subunit of a multicomponent protein. Even the smallest known genome of any free-living organism, Mycoplasma genitalium, contains 482 genes comprising 580,000 nucleotides.2

The decoding (translation) requires many components, including complex editing machinery to correct errors. But the famous philosopher of science, Sir Karl Popper (1902–1994), pointed out:

‘…the machinery by which the cell (at least the non-primitive cell, which is the only one we know) translates the code consists of at least fifty macromolecular components which are themselves coded in the DNA. Thus the code can not be translated except by using certain products of its translation. This constitutes a baffling circle; a really vicious circle, it seems, for any attempt to form a model or theory of the genesis of the genetic code.’3

The obvious conclusion is that the decoding must have been functional from the beginning, otherwise life could not exist.

Decoding molecules

One of the many types of molecules needed are the transfer ribonucleic acid (tRNA) molecules. These are the molecules which link the right amino acid with the right codon. They comprise about 80 nucleotide ‘letters’, three of which are called the anticodon. The anticodon links to the corresponding codon on the messenger RNA (mRNA), which in turn has relayed the correct code from the DNA. Thus the tRNAs can transfer the right amino acids to the right place in the growing peptide chain, as coded in the mRNA.4 Also, the amino acid is bonded to the tRNA in such a way as to be activated, i.e. to have a high chemical potential—this is necessary so it will form a peptide bond to the adjacent amino acid in the polypeptide. Free amino acids have almost no tendency to form polypeptides by themselves; rather, the tendency is for the reverse to happen.5
There are also enormous chemical hurdles for any evolutionary explanation of the origin of nucleic acids from a hypothetical primordial soup.6,7 And even if we granted that RNA could form spontaneously, there is a huge hurdle in linking the right amino acid to the right anticodon by naturalistic means. If the links are not correct, the entire decoding machinery would decode the wrong message, or no message at all, meaning that the organism could not manufacture vital enzymes. However, there is no chemical reason for any particular anticodon to link to any particular amino acid. In fact, they are at the opposite ends of the tRNAs, precluding any chemical interaction. Again, they must have been fully functional from the beginning.

Synthesizing the tRNAs

Living organisms do not, and could not, rely on random chemistry to synthesize the tRNAs. Rather, the right amino acid is activated and linked in two steps to the right tRNA by aminoacyl-tRNA synthetases (aaRSs).8 First, chemical energy is supplied by adenosine triphosphate (ATP), which was formed elsewhere by ATP synthase, an enzyme containing a miniature rotory motor, F1-ATPase.9,10,11,12 ATP reacts with the amino acid to form a mixed carboxylic-phosphoric anhydride.13 Secondly, the aminoacyl group forms an ester with the 3’-hydroxyl of the ribose in the terminal adenosine of the tRNA.8,13

Editing—double sieve enzymes

However, these steps are not enough to ensure the required high decoding fidelity (error rates of 1/2400 to 1/40,000). The aaRSs also edit the final products to make sure that the right amino acid is linked to the right tRNA. One difficulty is discriminating between chemically similar amino acids. In particular, L-valine (Val) and L-isoleucine (Ile) differ by only one methylene (CH2) group. Double Nobel laureate Linus Pauling (1901–1994), calculated that since the CH2 group has a hydrophobic binding energy of only about 4 kJ/mol, the error rate for replacing Ile with Val would be about one in five.14 So it is thermodynamically impossible for ordinary one-step recognition to achieve the error rate of 1/3,000 observed in isoleucyl-tRNA synthetase (IleRS).15,16,17,18

However, an error substituting Ile for Val can be biologically harmful or even catastrophic. Even a single Ile–Val mutation in the core of ribonuclease T1 reduces its stability because of ‘a loss of favorable packing interactions of the side chain in the folded form of the protein.’19 Such a mutation in the hydrophobic core of chymotrypsin inhibitor 2 changes the free energy of unfolding (DDGU–F) by 5.0 ± 0.4 kJ/mol on average.20 And a single Ile–Val mutation in the interior of human lysozyme results in less resistance to denaturation ((DDG from -1.5 – -5.0 kJ/mol).21 This mutation also increases susceptibility to lung cancer22 and affects Human Immunodeficiency Virus–1 drug resistance.23

Another problem cited by Pauling is that while an enzyme’s binding site can easily exclude molecules that are larger by steric hindrance, how can it exclude molecules that are smaller?14,15

Alan Fersht first proposed a solution in 1977: a ‘double-sieve’ editing mechanism.24 A coarse sieve would exclude larger amino acids from being activated, but allow the right amino acid and the smaller ones to be activated. Then a fine sieve would hydrolyse the products of the smaller amino acids (see diagram below).

Firgure 1: The double-sieve mechanism for the isoleucyl-tRNA synthetase. Hydrolytic editing reduces the error rate for the misactivation of valine from an expected value between 1 in 10 and 1 in 100 to 1 in 40,000 (after Ferscht15).

In 1998, Nureki et al. demonstrated this double-sieve mechanism in IleRS. They used X-ray diffraction (XRD) techniques to solve the crystal structure of Thermus thermophilus IleRS, as well as its complexes with Ile and Val. IleRS is a huge L-shaped molecule measuring about 100 Å x 80 Å x 45 Å , and belongs to the space group C2.8
IleRS contains a characteristic nucleotide binding fold, the Rossmann fold, in the centre. The ‘coarse sieve’ is a cleft in the Rossmann fold with two characteristic four-amino-acid sequences that bind ATP. The cleft also binds L-Ile at the bottom — its hydrocarbon groups and the NH3+ and COO– groups are recognized by strategically placed amino acid residues of the enzyme. This site is able to exclude larger amino acids by steric hindrance, including L-leucine, although this differs from Ile only in the placement of the methyl group on the side chain. This contrasts with ordinary laboratory organic chemistry, where ‘Leucine and isoleucine are particularly difficult to separate.’25

The fine sieve is another part of the Rossmann fold, the Ins-2 structural domain, which contains another deep cleft. XRD detected Val in this cleft in the L-valine-IleRS complex, but never any Ile in the L-isoleucine-IleRS complex — the cleft is simply too small. The incorrect Val products are hydrolysed here, but the correct Ile products are protected.

Nureki et al. demonstrated this by constructing a mutant IleRS which lacked 47 amino acid residues including a tryptophan (Trp232) of the L-valine-specific pocket.8 This completely destroyed the editing ability. In another experiment, Nureki et al. mutated just two amino acids (replacing Thr243 and Asn250 with alanine) of E. coli IleRS, which again completely destroyed the editing ability. Previous work had shown that even a single mutation (replacing Tyr403 with Phe) greatly reduces the editing ability of E. coli IleRS.26
Other aaRSs also have editing activity, including ValRS, which deacylates errant threonine products.27

Evolutionary bias

Unfortunately, the brilliant paper of Nureki et al.8 was spoiled when the authors went with the common secular flow, and genuflected to the idol of today—the Unholy Trinity of Time, Chance and Natural Selection. They wrote:

‘ … it is interesting from an evolutionary viewpoint that all of the enzymes catalyzing the central steps of Ile-Val biosynthesis and metabolism do not distinguish, or can neglect the difference, between the two aliphatic amino acids, as was observed for the first catalytic site of IleRS. This finding implies that a putative ancestral enzyme of IleRS and ValRS might have actually had a similar dual specificity for L-isoleucine and L-valine in a primordial genetic code system.’28

Of course, a good designer will often use similar machinery to make similar products,29 and it makes sense especially with the extremely close chemical similarity of Ile and Val.25 And their statement is merely ‘just-so’ story telling, lacking even the slightest evidence. It is no substitute for explaining exactly how such an editing site could evolve by natural selection. This site requires many amino acids in precise sequences before it could work at all, thus exhibiting a hallmark of design—what biochemist Michael Behe, in his book Darwin’s Black Box, termed irreducible complexity.30 The problem is especially acute in this case—since natural selection equals differential reproduction, if there is poor editing, then accurate reproduction of successful traits is impossible. Error catastrophe is more likely.29,31, 32

Popper, K.R., Scientific reduction and the essential incompleteness of all science; in Ayala, F. and Dobzhansky, T., eds., Studies in the Philosophy of Biology, University of California Press, Berkeley, p. 270, 1974. Return to text

Darwinists like to claim they can produce evidence some day that such complex forms happened by chance. What are the odds, being VERY KIND to the Darwinist point of view? (From a 2004 Jonathan Sarfati presentation in NSW, Australia).

10 to the 80th atoms in the Universe

10 to the 12th atomic interactions per second

10 to the 15th seconds in the Universe according to Big Bangers.

Therefore 10 to the 110 interactions possible.

There are 20 amino acid letters

Assume 256 enzymes for the simplest life (very generous here, too)

Give 10 conserved amino acids conserved on average.

Therefore the result is one chance in 10 to the 3330th! It would take a long time to write that number out, and that is to get just one simple cell, simpler than we have seen in real life, and naturally we have quadrilliions of organisms living on Earth right now. It doesn't add up even if the chemistry was not against the process.

Remember, oxygen kills off amino acids and prevents them from forming so they must form in anerobic environments and yet the oldest rocks show signs of the presence of oxygen.

Real science tells us that DNA base pairing is quite specific and brilliant coding. The information in the nucleus of one of your cells would make a pile of paperback books that would stack up to the Moon and back 500 times! The ATGC strand:

DNA's most amazing characteristic is that it will bind to itself in a very specific manner, forming a helix. Figure 1 illustrates two DNA molecules binding. The variable groups of the polymer interact with eachother to mediate this binding. Adenine interacts with Thymine and Cytosine interacts with Guanine. No other bonds are energetically favorable, for example Cytosine cannot bond with itself. The bonds that these variable groups form are called are called base pairs and are illustrated in Figure 2. Thus, by knowing the sequence of bases of one strand of DNA we immediately know the sequence of the DNA strand which will bind to it, this strand is called the reverse complement or just the complementary strand. In Figure 1 the right hand strand is the reverse complement of the left hand side and vice-versa.

DNA will bond in exact ways, helping to avoid copying errors while transmitting huge amounts of information. We use a two digit system to record information on computer hard drives and that is far less sophisticated. Eventually we may be able to copy some aspects of the DNA model to store and compute information more efficiently. Just as the Wright brothers studied birds to learn how to fly, we must study God's design if we want to learn a better way to do things.

Here is another factoid to chew on. ATP is a very complex engine working within your cells to ATP made half weight body in a day. Cyanide stops ATP from operating. In a human a fatal dose of cyanide kills in 30 seconds!

Do these statements need to be modified or are they universally general? e.g. do they apply to ocean vent biological systems?

Are there any detailed Neo-Darwinian mechanisms for the origin of ATP synthase?

The chemical reactions underlying this mechanical representation of the ATP process are another layer of complexity, as is the subject of water production during amino acid to protein processes and the remarkable instability of cytosine and chain termination by unifunctional compounds and the necessity of homochirality in amino acids and sugars or you get DNA or RNA chain termination as well and, well we could go on and on but enough for one night. But it should be obvious that it is Darwinists who are believing in Darwinism by faith and not by either logic or evidence!

14 comments:

Jon Woolf
said...

A very impressive example of the argument from personal incredulity.

Problem is, it doesn't work. All of this boils down to "I don't understand how life could have developed naturally, therefore it didn't." Not a scientific argument, Radar. And citing only creationist sources virtually guarantees that your facts are somehow flawed. Creationist authors lie whenever it suits their purpose.

"Darwinists have insisted that the Law of Biogenesis is not a law, even though it was declared a law in peer reviewed papers and official meetings and their publications after years of testing for, not just higher forms of life, but for the simplest of microbes."

The specific question was whether the impossibility of abiogenesis was declared a scientific law, which of course it wasn't.

If you think it was, please provide the evidence.

And of course even microbes can already be pretty complex.

"Since operational science has proven that life does not come from non-life, sterilizing and sealing off food from any source of contamination guarantees that no deadly bacteria will grow within the can of food unless the seal is broken. So any Darwinist who believes that canned food is safe is saying that he believes in abiogenesis but he is betting his health and perhaps his very life on the fact that abiogenesis will not happen! So my commenters are not practicing what they preach, so to speak."

Wow, this one has to go on Fundies Say The Darndest Things.

Radar, I don't know what kind of image you've built up in your head about these "Darwinists" and what they believe, but they certainly don't think that abiogenesis is about "deadly bacteria" (pretty complex life form there) sprouting over an afternoon in a jar.

Why are you so afraid of taking an open-minded look at subjects like abiogenesis or the theory of evolution?

It is I and not commenters who has an open mind about abiogenesis. This is not from personal incredulity but rather from a working knowledge of the behavior of amino acids and proteins and a bit of understanding of molecular biology.

Therefore the post does not boil down to my understanding, it is geochemical in nature. The raw building blocks of RNA and DNA cannot form in any conceivable natural circumstance because the way molecules perform in all of the proposed scenarios can be tested and falsified. All abiogenesis scenarios presented thus far have been falsified.

Creationist authors in fact are far less likely to lie than Atheists since they have a moral code established by God they respect and I have shown many times that Darwinists lie on purpose time and time again. So a creationist source is far more reliable.

Another problem with your arguments is that a great deal of my source material is from non-creationist sources. I notice you have no evidence to present so yet another fact-free argument from a Darwinist. Boring.

Sorry, Jon, but there are no Darwinist scientists yet who have come up with anything resembling an answer to how the components of RNA and DNA could be assembled in any natural way. Any reader who chooses to research on their own will find this out.

Especially ludicrous is the concept of life beginning in smoker vents. Chemical molecular biologists know they are stuck here. They do not wish to admit it because the wall is called design and they have no way around it. Rave and rant as you will the evidence will not change.

The problem with abiogenesis is that no one has presented so much as one plausible solution to the roadblocks that exist chemically to a natural formation of the RNA and DNA components, let alone the information they contain. It is not that I do not know, it is that the scientific world does not know and in fact is hopeless lost here. My next post will be another well-beloved copy from a scientific source that summarizes the complete lack of science involved in abiogenesis.

The law of biogenesis still stands unchallenged. Darwinism remains a fairy tale lacking the evidence needed to exist. It is propped up by worldview.

Radar,There's only one problem with your analogy about life not developing in a canned food. You forgot to include the time element. It is reasonable to assume that life will not generate spontaneously during our lifetime, but given (using my best Carl Sagan impersonation) "billions and billions" of years anything is possible, don'tcha know.

"The problem with abiogenesis is that no one has presented so much as one plausible solution to the roadblocks that exist chemically to a natural formation of the RNA and DNA components, let alone the information they contain. "

And if they ever do, you'll simply ignore it. You know it, and all of us know it too. You won't accept any solution as plausible except the one you've already assumed. Great theology, but rotten science.

I would just like to comment upon the fact that disproving another person's argument does not mean you have proven your own. You have built your argument around the structure of "X + Y could equal A and X + Z could also equal A. Therefore when X + Y is proven inaccurate X + Z = A." In your case, this is a logical fallicy because the argument is not limited to two options... rather X can be combined with an infinite multitude of letters.Regardless of whether or not your argument disproves abiogenesis, you haven't proven anything. So next time you want to post snide comments about another person's set of beliefs maybe you should present some evidence to support your own argument or else undecided people like me are going run to the more civil side of the argument which would in this case be the opposite of your standpoint. Do you want to convince people you are right? Then please discuss what others would regard as sensitive material in a manner that isn't insanely pompous and degrading because it gives Creationists a bad name and you're just fueling the same hate that was kindled by hundreds of generations of Christian oppression over scienctific discovery.

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